First, I dunno what you mean by "Secret PC", but I assume you mean the real PC and not the decoy.
You can delete that Secret Base, but it is tricky. You have to go into your PC, select "Manage Secret Bases", then select the Secret Base that is blocked and remove it. To find out what the Secret Base is, go and talk to all of the NPCs until you find the leader. Once you know his/her name, go and do the removal process.
This will remove those annoying inaccessible bases.